SMTL ID : 6q8w.2 (1 other biounit)

Respiratory complex I from Thermus thermophilus with bound Aureothin.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

7 x SF4: IRON/SULFUR CLUSTER(Covalent)(Non-covalent)

SF4.1: 11 residues within 4Å: Chain A: P.199, S.352, C.353, G.354, K.355, C.356, C.359, S.398, F.399, C.400, A.403 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.353, A:C.356, A:C.359, A:C.400 SF4.4: 11 residues within 4Å: Chain C: H.115, D.118, C.119, C.122, C.128, L.130, Q.131, R.180, V.232, G.233 Chain D: I.325 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D, Metal complexes: C:H.115, C:C.119, C:C.122, C:C.128 pi-Cation interactions: D:F.328 SF4.5: 10 residues within 4Å: Chain C: C.181, I.182, H.183, C.184, R.186, C.187, C.230, V.232, A.234, L.235 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.181, C:C.184, C:C.187, C:C.230 SF4.6: 11 residues within 4Å: Chain C: C.256, L.258, C.259, V.261, G.262, C.263, I.290, C.291, G.294, P.407, I.408 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.256, C:C.259, C:C.263, C:C.291 SF4.9: 13 residues within 4Å: Chain D: R.84, H.169 Chain F: C.45, C.46, G.82, R.83, A.110, C.111, F.118, G.139, C.140, P.141 Chain G: I.99 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.45, F:C.46, F:C.111, F:C.140 SF4.10: 11 residues within 4Å: Chain G: H.41, A.62, C.63, P.64, I.68, C.98, I.99, F.100, C.101, G.102, C.104 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.63, G:C.98, G:C.101, G:C.104 SF4.11: 12 residues within 4Å: Chain G: C.53, I.54, G.55, C.56, S.57, L.58, C.59, Y.91, C.108, P.109, T.110, I.113 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.53, G:C.56, G:C.59, G:C.108

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 16 residues within 4Å: Chain A: G.64, R.65, G.66, A.68, K.75, N.92, D.94, S.96, Y.180, G.183, E.184, N.219, N.220, T.223, P.401, L.402 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.401, A:L.402 Hydrogen bonds: A:G.66, A:A.68, A:N.92, A:D.94, A:D.94, A:S.96, A:G.183, A:N.219, A:N.220, A:N.220 Salt bridges: A:K.75

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.3: 9 residues within 4Å: Chain B: C.83, T.85, S.87, C.88, C.124, L.125, G.126, S.127, C.128 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.83, B:C.88, B:C.124, B:C.128 FES.7: 8 residues within 4Å: Chain C: C.34, S.35, G.43, A.44, C.45, R.46, C.48, C.83 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.34, C:C.45, C:C.48, C:C.83

1 x HQW: Aureothin(Non-covalent)

HQW.8: 15 residues within 4Å: Chain D: Q.33, H.38, G.39, V.40, Y.87, T.135, F.146, F.147, P.402 Chain F: L.43, A.47, M.51, T.54, F.68 Chain P: Q.226 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:F.146, F:F.68 Hydrogen bonds: D:G.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gutierrez-Fernandez, J. et al., Key role of quinone in the mechanism of respiratory complex I. Nat Commun (2020)

Release Date

2020-09-02

Peptides

NADH-quinone oxidoreductase subunit 1: A
NADH-quinone oxidoreductase subunit 2: B
NADH-quinone oxidoreductase subunit 3: C
NADH-quinone oxidoreductase subunit 4: D
NADH-quinone oxidoreductase subunit 5: E
NADH-quinone oxidoreductase subunit 6: F
NADH-quinone oxidoreductase subunit 9: G
NADH-quinone oxidoreductase subunit 15: H
Uncharacterized protein: I
NADH-quinone oxidoreductase subunit 7: J
NADH-quinone oxidoreductase subunit 10: K
NADH-quinone oxidoreductase subunit 11: L
NADH-quinone oxidoreductase subunit 12: M
NADH-quinone oxidoreductase subunit 13: N
NADH-quinone oxidoreductase subunit 14: O
NADH-quinone oxidoreductase subunit 8: P

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
E

E
F

F
G

G
O

H
I

I
X

J
P

K
R

L
S

M
T

N
U

O
V

P
Q

Membrane

We predict this structure to be a membrane protein.
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NADH-quinone oxidoreductase subunit 1

NADH-quinone oxidoreductase subunit 2

NADH-quinone oxidoreductase subunit 3

NADH-quinone oxidoreductase subunit 4

NADH-quinone oxidoreductase subunit 5

NADH-quinone oxidoreductase subunit 6

NADH-quinone oxidoreductase subunit 9

NADH-quinone oxidoreductase subunit 15

Uncharacterized protein

NADH-quinone oxidoreductase subunit 7

NADH-quinone oxidoreductase subunit 10

NADH-quinone oxidoreductase subunit 11

NADH-quinone oxidoreductase subunit 12

NADH-quinone oxidoreductase subunit 13

NADH-quinone oxidoreductase subunit 14

NADH-quinone oxidoreductase subunit 8

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